The goal of this work was to nondestructively measure glomerular (and thereby nephron) number in the whole kidney. Variations in the number and size of glomeruli have been linked to a number of renal and systemic diseases. Here we develop a robust magnetic resonance imaging (MRI) technique based on injection of cationic ferritin (CF) to produce an accurate measurement of number and size of individual glomeruli. High-field (19T) gradient-echo MR images of perfused rat kidneys after in vivo intravenous injection of CF showed specific labeling of individual glomeruli with CF throughout the kidney. We developed a 3D image processing algorithm to count every labeled glomerulus. MRI-based counts yielded 33,786+/-3,753 labeled glomeruli (n=5 kidneys). Acid maceration counting of contralateral kidneys yielded an estimate of 30,585+/-2,053 glomeruli (n=6 kidneys). Disector/fractionator stereology counting yielded an estimate of 34,963 glomeruli (n=2). MRI-based measurement of apparent glomerular volume of labeled glomeruli was measured to be 4.89x10(-4) mm(3) (n=5), compared to the average stereological measurement of 4.99x10(-4) mm(3) (n=2). The MRI-based technique also yielded the intra-renal distribution of apparent glomerular volume, a measurement previously unobtainable in histology. This work makes it possible to nondestructively measure whole-kidney glomerular number and apparent glomerular volumes to study susceptibility to renal diseases and opens the door to similar in vivo measurements in animals and humans.